Darker Star
by johnliz4ever
Summary: The Atlantis team comes home and an whole new story begins. Crossover with SG1.JohnLiz, JackSam tension, JackLiz. Rating may go up
1. Chapter 1

Disclaimer: I don't own Stargate Atlantis or SG1

Note: Not beta'd so all mistakes are my own. **Also as it appears that this needs to be stated. This Fic is AU, it takes place years into the future. Things have changed, people have change. Just because somebody wouldn't have done something back during season 2 Atlantis doesn't mean they won't do it 5 years into the future. **  
Pairing: John/Liz, Jack/Sam tension, Jack/Liz (Not quite sure in what context yet)  
Spoilers: To be safe up to and including season 2 Atlantis and season 9 SG1

**Darker Star **

**Cheyenne Mountain Complex **(June 4th 2010)

Jack pulled a chair up to the infirmary bed and looked at the small fragile woman that was lying on it. He hadn't seen her in nearly 6 years but he could tell she'd been through the mill a few times. She had a black eye, a swollen cheek, 3 broken ribs one of which had punctured her lung and a sprained ankle. She was not looking her best. He placed his hand over hers and sighed. What had they done to her?

He heard someone enter the infirmary and he quickly moved his hand from hers. He looked and saw Sam walking towards them. She looked at Elizabeth, sighed then looked at Jack.

"How's she doing?"

Jack sighed. He knew Sam didn't care for Elizabeth but he also knew she wouldn't wish this on anyone.

"It looks bad and it is bad."

Sam sighed and sat next to Jack.

"I don't like her that much, but she shouldn't have had to go through this"

She looked at Jack and he was sure that, just for a second he could see a few tears form in her eyes before she quickly pushed them away. Jack cleared his throat and drew his gaze away from Elizabeth.

"How's Colonel Sheppard?"

Sam sighed.

"He's damaged more emotionally then physically. He's worried about Dr Weir, he wants to see her"

Jack nodded and stood up.

"I'll go and see him, will you stay with Weir? I don't want to leave her alone; if you don't want to I can get Daniel"

Sam nodded.

"It's okay, I'll stay here"

Jack smiled and left the infirmary without another word. Sam looked at Elizabeth and sighed, seeing her like this had really unsettled Jack and the worse thing was he didn't know what had happened. Nobody that had survived the expedition were up to talking and many of them were going to have trouble surviving through the night.  
Only twenty came back, twenty of nearly 200.  
Dr Beckett didn't make it, neither did Lt Ford. St Stackhouse didn't come back and neither did Dr Heightmeyer.  
She sighed, apart from Elizabeth and John, Rodney had made it back, an alien name Teyla, St Bates and some more scientists and a few military.  
When she saw them come through the 'Gate she was overcome by shock at their appearance and terrified when Elizabeth collapsed onto the ramp.

**:Flashback:**

**Cheyenne Mountain Complex **(June 3rd 2010)

The Stargate began to spin, the technician put the iris up, Sam, Jack, Daniel, Teal'c and Cameron entered the control room. Sam sat next to the technician and the Stargate engaged.

"Any IDC?"

Sam turned and looked at Jack.

"Not yet Sir"

The technician turned to Sam.

"Wait, we're receiving an IDC…It's Atlantis"

Jack began to walk down to the 'Gate room shouting over his shoulder at the same time.

"Open the iris"

Sam, Daniel, Teal'c and Cameron followed him down to the 'Gate room.

The iris opened and a few seconds later, someone walked down the ramp, followed by another and another. They were battered and bruised, their clothing was ripped, they were helping each other stand. Sam watched in shock as she saw a very dishevelled Rodney McKay walk through the 'Gate. She was expecting a smirk or something that was McKay but instead she could see he was broken, deep lines were around his eyes; he had a bruise on his cheek and was limping. This was not the man she knew.

Then she saw two men walk through supporting the small frame of a woman. She immediately identified the two men as Colonel John Sheppard and St Bates but she couldn't make out who the woman was, as the last of the people walked through John turned to Jack.

"Close the iris"

His voice was quiet, weak and broken; Jack shouted the order for the iris to be closed. The small woman who was being held by Bates and John suddenly fell from their arms onto the ramp. Jack quickly called a medical team as John fell to the woman's side.

"Elizabeth, Liz"

Sam froze as she heard John call Elizabeths' name. That was Elizabeth Weir. That small, fragile woman was Dr Elizabeth Weir. Sam snapped out of her trance and saw Jack rush over to the fallen Elizabeth and check her pulse. His gaze fell onto John as if assigning blame onto him. As the medical team entered Jack immediately lifted Elizabeth into his arms, put her on the nearest stretcher and ordered that she be looked at first. He then turned to John who was sat on the edge of the ramp breathing heavily; Jack softened and placed his hand on John's shoulder then helped him to his feet.

"Get yourself into the infirmary"

John nodded and followed the rest of his team out of the 'Gate room.

Jack watched him go and sighed. He ran his fingers through his hair and left the 'Gate room without a word to SG1. Cameron turned to Daniel.

"What the hell was that?"

Daniel turned to him, tears in his eyes.

"That was probably the last of our expedition team."

Daniel left the 'Gate room followed by Teal'c. Cameron and Sam shared a look before leaving the 'Gate room themselves.

**:End of Flashback:**

The door to the infirmary opened and Cameron Mitchell walked in and sat next to Sam in the seat that Jack had just vacated.

"How's she doing?"

Sam sighed.

"Not good"

Cameron nodded. He'd seen some horrific things during his time at the SGC but nothing like this. He couldn't remember Jack being as freaked as he was in the control room. Cameron looked at Elizabeth and instantly got the wrong idea.

"What went on between the General and her?"

He nodded towards Elizabeth and Sam shook her head.

"Nothing went on between them, why would you think that?"

Cameron shook his head,

"I just thought…you saw the way he reacted…it was…intense"

Sam shook her head.

"General O'Neill would be like that if it was anybody."

Cameron nodded and left his seat.

"I guess; it was just…that look in his eyes when she collapsed, he looked devastated"

Cameron left the room leaving Sam to contemplate what he'd just said. Sure Jack had been unsettled when he saw the team come through the Stargate and yes, he did seem very concerned about Elizabeths' wellbeing, but it was just professionalism, wasn't it?

TBC…

Do you want me to continue? Please no flames about killing off Ford, Beckett, Stackhouse and Heightmeyer. I've already flamed myself for doing that, but I had too.


	2. Chapter 2

Disclaimer: I don't own Stargate Atlantis and SG1.

Note: Thanks for the reviews, glad you're liking it so far. I'm glad I've already got people thinking about the Jack/Liz thing, but I'm not giving away any secrets.

As Jack left the infirmary, he passed Cameron Mitchell and kept walking. A part of him didn't want to know what his people had been through, something told him it was so horrific, so painful and something none of them would get over. He walked round the corridors to the guest room where they were keeping John. He knocked on the door and entered, he saw a nurse dressing one of John's wounds. Ideally he would have been in the infirmary but John's injuries were minor, physically anyway, and the infirmary was filled to capacity. Jack leant against a table on the far side of the room and watched as the nurse finished dressing his wound. She then left the two of them alone with an order that John rest.

Jack pushed himself off the table and went too sat on the chair next to John's bed. They stayed silent for a few moments, each not knowing what to say to the other. John cleared his throat and finally broke the silence.

"How's Dr Weir?"

Jack sighed and looked down at his hands. He didn't know whether telling John would be a good idea, he was weak and hearing about Elizabeth would only make things worse. But then again if he'd survived whatever the hell they'd just been through, he'd be able to survive this.

"She's not good, she has a punctured lung, several broken ribs and a sprained ankle, she's got a hell of a lot of buries as well."

It was John's turn to look down at his hands now as his voice, barely above a whisper answered Jack.

"Can I see her? I want to be with her when she wakes up"

Even though he couldn't see his eyes he knew they were filling up with tears. He could hear the shakiness in his voice, Jack knew it was entirely possible that Elizabeth wouldn't survive the night and he also knew that even though John was suppose to be resting he wouldn't while Elizabeth was laying in an infirmary bed fighting for her life. Jack nodded.

"After you've seen her you need to rest, I need you to tell me what happened"

John's whole body tense, the thought of relieving what they'd been through was terrifying to him. All the pain, the screams, the death. John had seen it before, but nothing that bad, nothing that evil. John nodded slowly and got off the bed, the side of his torso protesting slightly, Jack saw John wince and quickly went to his side and helped support him.

"Easy, take your time"

John let Jack take some of his weight, thankful he was there.

"Do you want me to get you a wheelchair of something?"

John shook his head.

"No, no I'm good; the morphine will kick in soon"

Jack nodded and slowly helped John from the room to the infirmary. Jack was not surprised that John hadn't shown signs of being hurt when he came through the 'Gate, sometimes adrenaline was the best drug.

As they entered the infirmary, Sam immediately stood and helped John to sit down. When John was sat down he gripped Elizabeth's hand, Jack and Sam slipped out of the infirmary feeling as if they were invading a private moment. From where they were stood they had a clear view into the infirmary, they saw John pick up Elizabeth's hand and kiss it, still holding her hand, he quietly prayed. Jack looked over that the two of them. John obviously cared deeply about her, not that he could blame him, Elizabeth had a way of working herself into your heart and staying there.

Jack quickly pushed back his feelings and turned to Sam.

"I'm gonna go call the President. Let me know if she wakes up"

With that, Jack disappeared around a corridor. She stood there outside the infirmary for a few more moments thinking about what Cameron had said. She couldn't get it out of her mind. He couldn't, Jack would have been like that for anyone that looked as beaten as she did. She closed her eyes but was suddenly conscious of another person standing with her, she opened her eyes and saw Rodney, his eyes were gazing into the infirmary and before Sam could even say something, he asked, in a quiet voice…

"How is she?"

Sam could hear the unshed tears in his voice, what was it about this woman that could trapped men? John, Jack, Daniel, Rodney and she was beginning to suspect Cameron and he didn't even know her.

Sam answered in an equally quiet voice.

"Not good Rodney, I'm sorry I wish I had better news."

Rodney wasn't listening to her though, his eyes were clearly fixed on the two people in front of him.

"You know, if she doesn't survive, neither will he, they've been each others strength these last few months…" Rodney looked down at his hands "…she's been everybody's strength…she's helped us through everything, anger, sadness, depression…" Rodney's eyes began to fill up with tears; as if there were things he wasn't telling her "…she's never given up on any of us or herself…" He turned to Sam sharply "…promise me she'll live"

Sam closed her eyes and placed her hand on his arm.

"I can't do that Rodney"

Rodney pushed her hand from his arm and walked into the infirmary. He sat next to John silently, each of them just watching Elizabeth, begging her silently to pull through. Rodney placed his elbows onto the edge of her bed, clasped his hands together and silently prayed like John had moments before.

_If you're up there and you can hear me, you know she doesn't deserve this, she doesn't deserve die like this. Please don't take her from us, we treasure her, she's one of your most precious angels and when the time comes you can take her back, but please don't make that time now, she should be old and warm in her bed, she should die peacefully not like this. _

Maybe it wasn't the best prayer in the world but he meant the words. If angels were among them, there was no doubt in his mind that Elizabeth was one.  
During all the things they'd seen, the things done she'd never lost faith. She'd been strong, to him that made her an angel.

* * *

Jack put down the phone and sighed. The President had told Jack the same as he did the day before when Jack had called him to inform him of their arrival. He was sympathetic to their current situation, the leader of the expedition laying with a punctured lung in the infirmary, but he wanted answered, the Joint Chiefs wanted answers, they wanted to know whether Earth was at risk, Jack had assured them again that if they were in any immediate danger Colonel Sheppard would have informed them straight-away. He didn't mention that John Sheppard wasn't thinking straight at the moment but he assumed it was suspected. 

Jack sighed and rubbed his forehead. He had to schedule a briefing and one he wasn't looking forward too, but he had to know what had happened to his people, to John, Rodney and of course Elizabeth. Jack took two aspirin from his drawer and swallowed them. This was one hell of a headache he wasn't expecting.

* * *

Jack slipped out of his office and walked down the corridors, as he neared the infirmary he saw Sam standing outside. He stood next to her and saw Rodney and John sitting silently with Elizabeth. Jack walked into the room past Sam, as he entered the room, John went to stand and Jack immediately stopped him. 

"At ease Colonel."

John nodded and sat back down. Jack looked at the men in the room, they both seemed tired and beaten down, only holding onto the hope and the faith that she would pull through.

Jack cleared his throat.

"Colonel Sheppard, Dr McKay, I know this is a bad time but the Joint Chiefs want to conduct a briefing tomorrow afternoon with both of you in attendance."

Jack received looks of disbelief from Jack and Rodney.

"Sir, with all due respect, how can they expect us to be in a meeting without Elizabeth in attendance?"

Jack sighed.

"Colonel, I know it is not an ideal situation but the Joint Chiefs want to know if there is any immediate danger to Earth and its allies"

Rodney stood up in disbelief.

"If there were any _immediate _danger don't you think we would have said something straight-away, just so we don't have to relieve what happened to all of us, what happened to Elizabeth?"

John stood up and put his hand on Rodney's shoulder.

"Rodney, it's okay."

John turned to Jack.

"Fine, we will attend a briefing."

Jack nodded and after taking one last look at Elizabeth, he left the infirmary. John and Rodney sat back down next to Elizabeth and continued the silent watch.

TBC…


	3. Chapter 3

Disclaimer: I don't own Stargate Atlantis

Note: Thanks for the reviews and I have finally decided what I'm going to do with Liz and Jack.

**Cheyenne Mountain Complex **(June 5th 2010)

Lt Colonel John Sheppard sat patiently in the briefing room with all the surviving members of his team who were well enough to attend. While Elizabeths' condition was the worse, several scientist and Marines were still unable to leave the infirmary meaning only John, Rodney, Teyla, St Bates and Dr Zelenka were present at the briefing.

Rodney was fidgeting next to John,

"McKay pack it in"

There was no real force behind his words but it still caused Rodney looked up at him; he could clearly see that John was agitated. He hadn't wanted to leave Elizabeth to attended this briefing but while Elizabeth was incapacitated he was the most senior member of the team, meaning he was the one with his head on a platter if the Joint Chiefs didn't like what he had to say.

Rodney quickly stopped his fidgeting and sat still.

The door to the briefing room opened and Jack walked in followed by the Joint Chiefs, John, ignoring how his side was protesting, and Bates stood up immediately followed somewhat sluggishly by the non-military members of the room. John and Bates saluted simultaneously and it was returned by Jack and the Joint Chiefs.

"Colonel Sheppard, St Bates. At ease"

John, Bates and the team sat down, a moment later Jack and the Joint Chiefs followed suit. Jack cleared his throat.

"I think firstly we should give you are condolences for the members of the expedition that were lost. Their sacrifice shall not go unforgotten."

John nodded.

"Thank you Sir"

Jack nodded and began again

"And I think I speak for everyone when I say that I hope Dr Weir will pull through without any serious complications"

John saw the look in Jack's eyes and was shocked. His eyes were dark, as if he was trying to block out any emotions he was feeling. John shook his head; he was being irrational.

Jack turned to John.

"Colonel, I think the first thing we should concern ourselves with is what happened before you stepped through that 'Gate and how.

John nodded and cleared his throat; he received a look of support from Rodney, and closed his eyes before beginning.

"We were caught up in midst a war, the likes of which nobody from Earth has ever seen. Twenty Wraith Hive Ships were coming, we'd never had to deal with that kind of opposition before, we didn't stand a chance so we decided to destroy the city. Drs McKay, Zelenka, Simpson and Kavanagh were working on how to increase the explosive power of our self destruct system while myself, St Bates, Lt Ford, St Stackhouse, Teyla, Colonel Caldwell and Dr Weir set C-4 charges all around this city…"

**:Flashback:**

**Atlantis **(June 3rd 2010)

The early morning sunshine shone onto the many balcony's of Atlantis but there was no time to enjoy it.

Elizabeth stood in front of the final members of her city, only 50 of them were left, 50 people that may not survive.

"I know we have expected this coming for a long time and I know we have done everything in our power to stop it, we can't give up. I know you are all tired and I know we're all scared but we have to believe that we will survive."

She looked to John and he gave her a supportive smile, she returned it and looked back at her team.

"Rodney, Radek, Simpson and Kavanagh I need your team to keep working on increasing explosive power of the self destruct as much as you can even a small percentage will greatly help."

She turned to John, Ford and the team.

"Colonel Sheppard, Colonel Caldwell, I want your team to continue placing C-4 around the more sensitive areas of Atlantis. If the Wraith want this place in one piece I intend to disappoint them"

John and Caldwell nodded.

"Yes Ma'am"

John looked straight into her eyes and she looked into his. They were both determined to make sure their people survived this.

While Rodney and the scientists disappeared in one direction, John, Elizabeth and the military team headed off in another.

"We'll set the charges to go off by remote control, keep your radios on, two clicks and you're clear to talk"

Caldwell laid down the rules while the rest of the team listened attentively.

"Groups of two and cover as much of the city as possible"

Elizabeth and John instantly teamed up, as did Teyla and Ford. The rest of the team got into pairs and went their separate ways.

As John and Elizabeth got further away from the group he glanced at her, she'd changed. She now carried a weapon but after all the attacks on Atlantis in recent months he couldn't blame her. She'd given the order two days before when a ZPM had been found that they were going back to Earth. No arguments. They couldn't stay.

John was broke out of his musing when he saw something out of the corner of his eye. He grabbed Elizabeths' arm and stopped her. She turned back to him and he gestured next to him. They curiously sneaked around the corner and John took out a life signs detector, there was something in their immediate position and they shouldn't have been.

He picked up his radio and quietly whispered.

"We have unidentified targets in the city, be on your guard, all of you"

Two taps came over the radio followed by Fords' voice.

"Understood sir, you two be careful"

John and Elizabeth walked into the direction of the target. As they slipped around the corner, they saw the target. John aimed his P-90 and Elizabeth picked up her radio.

"We have Wraith in the city; I repeat there are Wraith in the city"

Suddenly uncountable amounts of shots were heard from next to Elizabeth, she turned round and saw John lowering his P-90, he turned to her. It had to be done, she knew that, but even though she carried and used a gun, there was still something about them which made her uneasy.

"Let's go"

* * *

John and Elizabeth slipped around the city setting charges in pre-determined places. As they were nearing their final position, they heard gunfire that quickly silenced. Ford and Teyla were the nearest to their position. 

"Ford, Teyla what was that? Ford, Teyla please respond"

The only response they received was static. John and Elizabeth shared a look, John quickly set the last charge and he and Elizabeth headed off to direction the gunfire had come from moments before.

They ran, faster and faster. John took out his life signs detector again and saw that there were five targets a few corridors away from them. The five targets were stationary and John concluded that it had to be either Ford and Teyla or Wraith.

They quickly made their way to the targets and stopped when they saw what was happening. There were three Wraiths plus Ford and Teyla. Two of the Wraiths were holding Teyla while the third was sucking the life out of Ford. John froze, no it couldn't be happening again, not another one. John lifted his P-90 but his finger froze on the trigger. He was flooded with the memory of Colonel Sumner. Of his finger pressing against the trigger ending his life.

John couldn't bare to take another life, he couldn't. Ford was dead he knew it, Elizabeth knew it, Teyla and Ford knew it, but he couldn't bare to do it. Ford was going to suffer and there was nothing he could do about it. John closed his eyes, a shot rang out and John quickly opened his eyes. He saw Elizabeth stood next to him, tears falling from her eyes and freshly fired gun in her hands. He looked over and saw both Ford and the Wraith laying on the floor, both dead.

John gazed back over to Elizabeth, she didn't, she couldn't have. Quickly John snapped out of his thoughts and shot the two guards standing either side of Teyla. The Wraith fell down and stayed down. John rushed to Teyla and helped her to stand up. Teyla got to her feet and steadied herself. Then she saw him, laying on the floor dead. She rushed to Fords side.

"Aiden, Aiden wake up…please…wake up"

She knew he was dead. Tears formed in her eyes and John dragged her away from Ford. She tried to fight against him but she was too upset to fight for long. John held Teyla tightly in his arms and he gazed over to Elizabeth who simply closed her eyes, causing her more tears to fall from her eyes, and walked away from them.

* * *

John and Teyla walked into the lab where Rodney and the scientists were working on the self-destruct. John hadn't been able to find Elizabeth since the incident with Ford. He figured if she was anywhere she'd be there. He sat Teyla down near and gazed around the room. He couldn't see Elizabeth or Rodney. 

He went over to Zelenka.

"Radek, as Elizabeth come in here?"

Redek nodded.

"Yes, she's with Rodney in his office. She looked upset."

John nodded and went over to Rodney's office; he opened the door slightly and saw Elizabeth, her head in her hands and Rodney gently rubbing her back.

"You did the right thing Elizabeth. I know Ford wouldn't have wanted to die at the hands of a Wraith."

Elizabeth lifted her head and looked at Rodney.

"That doesn't make it right. I've never killed anybody before Rodney. The look in Teylas' eyes when she saw him. She was devastated."

Elizabeths' sobs became harder and Rodney pulled her into a hug.

"It's okay Elizabeth, it's okay."

John shut the door and fought back his own tears. He knew Elizabeth would feel guilty about it but he didn't understand just how guilty she'd feel. She took a life, she took the life of her friend, someone she cared about. He had a feeling she wouldn't bounce back from that very easily.

John gazed over the lab, Kate was sat with Teyla trying desperately to comfort her, the scientists were putting the finishing touches to the self-destruct and the rest of the military personal were beginning to assemble. It was going to be the fight of their life.

**:End of Flashback:**

John pushed back the tears which were forming in his eyes again, he wasn't even half-way through what happened that day, there was so much loss, so much sadness that day. He didn't know if he could talk about it anymore, he knew they wouldn't understand, how could they?

Jack saw John fall, heard how his voice cracked when he talked about Elizabeth firing that deadly shot. He had no idea what they'd been through, only they did. He knew Elizabeth wouldn't have fired that shot without thinking of the consequences first. He knew in the same position, he'd have fired that shot as well.

TBC…

I'll conclude with the flashbacks next chapter.


	4. Chapter 4

Disclaimer: I don't own Stargate Atlantis or SG1 but I would like them to put Elizabeth, John and Jack in a room together and see what happens.

Note: Thanks for the reviews and I'm glad you're enjoying it. Also to Dark Faith 5 just so you know I'm not becoming a Jack/Liz shipper. My heart still belongs to and will always belong to Shweir, it's just I can have a bit fun with Jack/Liz.

* * *

John cleared his throat. Jack and the Joint Chiefs had called for a small break and John was more than happy. He made his way into the infirmary and sat next to Elizabeth. He wanted her to wake up so he could tell her that he didn't blame her, that she had done what was necessary, that she'd done what anyone would have done in her position. He grabbed her hand and held it tightly. 

Tears threaten to fall from his eyes but he keeps them locked up. He doesn't want her to see him cry. He wants to be strong for her.

Jack walked into the infirmary and saw John holding Elizabeths' hand, tighter then what was strictly necessary. He walked over to him and placed a hand on his shoulder. John looked up at him, his tears clouding his eyes. Jack sat down in the seat next to John and sighed.

"Tell me what happened John. Afterwards."

John looked over at Elizabeth.

"Teyla was so upset; she knew Elizabeth was the one that fired the shot. She was angry."

**:Flashback: **

**Atlantis **(June 3rd 2010)

Elizabeth and Rodney eventually left his office. She'd stopped crying and the redness in her face had gone. Rodney placed his hand on Elizabeth back and led her over to a nearby chair. Across the lab, Teyla had seen Elizabeth leave Rodney's office. She was insane with rage. Elizabeth had to pay; she had killed Aiden.

By now, everyone knew that Elizabeth had fired the shot, which had killed Aiden so it was no surprise when Teyla left her seat and walked over to Elizabeth.

If Elizabeth was completely honest with herself she expected the fist that connected with her cheek.

Elizabeth stumbled back off her seat at the force of the hit. Caldwell was immediately at her side, helping her up.

Teyla looked at her.

"You killed him. You are no better than the Wraith."

Tears began to swell up in Elizabeth's eyes.

"I'm sorry Teyla, I'm so sorry."

The tears fell from Elizabeth's eyes.

"He could have lived. It was possible but you destroyed all chance of that."

Elizabeth got to her feet and faced Teyla.

"He wouldn't have lived Teyla, you know that. He was nearly dead anyway."

Teyla hit Elizabeth again. This time she skimmed her eye.

Something in Elizabeth snapped. She'd done what she thought was best, she'd put everyone else's life in front of her own these past few months. She'd let them shout at her, get angry at her, cry on her shoulder. She'd had enough.

"Would you have preferred him to die at the hands of a Wraith? Like Halling did, like your parents did"

Caldwell, sensing this was going to end worse for Elizabeth than Teyla turned to Sheppard.

"Sheppard get her out of here."

John nodded and grabbed Teyla. Teyla reluctantly left the infirmary while Caldwell and Rodney tried to bring down the swelling in Elizabeth's cheek.

John led Teyla away from the lab and turned to her.

"What the hell was Teyla? I know you are upset, I am too, but what you did was unacceptable"

Tears had finally left Teyla's eyes and now it was replaced by anger.

"She killed him. She deserves to pay"

John shook his head.

"She saved him. I saw the look in Sumner's eyes when the Wraith was feeding on him. It was pure terror. Now Teyla, there are Wraith in the city. Get it together and stay away from Weir"

Teyla nodded sharply before walking back into the lab. John sighed turned round and followed her.

When he walked back into the lab he saw Caldwell gently pressing a cold towel to Elizabeth's very swollen cheek and black eye. Elizabeth winced and Caldwell apologized, John walked over to them.

"Are you okay Elizabeth?"

Caldwell, rather sharply answered for her.

"What do you think Sheppard?"

Elizabeth couldn't even bare to make eye contact with John. He nodded and let the two of the alone.

**:End of Flashback:**

Jack sat attentively listening to Johns' every word. When he stopped talking Jack cleared his throat.

"So she got the swollen cheek and black eye from Teyla?"

John nodded

"She was upset. Teyla and Ford are…were close."

Jack nodded showing John he understood. The hell those people had been through was something none of them would ever be able to understand. Sure SG1 had been in some tight spots before but Jack had never seen anyone as broken as these people were.

Jack looked over at Elizabeth. She was weak, broken, not the same woman he knew. He didn't know whether she'd be that woman again. She'd taken a life and while he understood it was done to show Ford mercy, he also knew that the first time you shot someone, friend or no, Jack knew how difficult it was to cope with killing another person.

Jack looked at how tired John was. He sighed; the damn Joint Chiefs could wait. These people needed to rest.

"John, go get some rest."

John shook his head. His eyes firmly fixed on Elizabeth.

"No I have to be here when she wakes up"

Jack easily pulled John from his seat, showing him how weak he was.

"John, you're exhausted. You're no use to anyone in this condition. Get some rest then come back later. I'll stay with Elizabeth"

John sighed and looked at Elizabeth

"What about the Joint Chiefs?"

Jack shook his head

"I'll take care of the Joint Chiefs"

John nodded before bending over and kissing Elizabeth on the forehead completely oblivious to the fact that he was being unprofessional while his CO was in the room.

Jack knew John held some feelings for Elizabeth and was not surprised by it. Elizabeth was the type of woman every man could find himself loving. She could be professional but still fun; she was strong but still had a side that needed protecting.

Jack knew this well, probably better than anyone on the base, including John.

Jack looked back at John as he whispered in Elizabeth's ear.

"I'll be back later, feel free to wake up anytime."

John gave Jack a small smile before leaving the infirmary. Jack watched John leave before sitting in the chair he'd just vacated and picking up Elizabeth's hand,

"You know you have to wake up don't you. There's too may people here that'd be upset if you didn't. You're the heart and soul of these people. They need you Elizabeth…" Jack looked down at their intertwining hands and added quietly. "…I need you to wake up Elizabeth"

* * *

Rodney left his temporary quarters and walked around the corridors of the SGC. He had to sort this out otherwise it would escalate and he couldn't let that happen. He walked until he reached the target he was looking for. He looked at the metal door before knocking on it. The door opened to reveal a teary-eyed Teyla. 

"Rodney, what can I do for you?"

Rodney sighed

"Can I come in?"

Teyla nodded and moved to allow him entry before closing the door and sitting over on the bed.

"How can I help you?"

Rodney looked at Teyla before going and sitting next to her. He thought for a moment before taking her hand in his. The two of them were good friends and he just hoped she'd hear him out.

"Teyla, you can't hold it against her, she did what she thought was best"

Teyla stood up and drew her hand back from him.

"I do not want to discuss this"

Rodney stood up and grabbed her arm.

"You are not the only person who as lost somebody. I've lost Kate and Carson. The two people I cared the most about and they suffered…"

Rodney was cut off by Teyla.

"…But they were not killed by the person you consider to be your closest friend"

Rodney jumped back in

"You're right they were, they were killed by the Wraith and I would have done anything to save them from that including killing them myself but I couldn't. Elizabeth showed mercy. You know she cared for Aiden and let him die the way he would have wanted to given the options he had."

Teyla looked down

"We have to all stick together Teyla. All of us, we don't know what they are going to do to us."

Teyla looked back up at him before moving over to him and burying her head into his chest. Rodney moved his arms around her waist and held her as she slowly allowed her tears to fall, accompanied by several of his own.

**

* * *

:Flashback: **

**McMurdo Air Force Base, Antarctica **(July 17th 2004)

Jack sat opposite Elizabeth, wondering if she was clinically insane.

"You really want him on this expedition don't you?"

Jack hadn't managed to convince John Sheppard to go on the expedition but Elizabeth was still adamant that she wanted him there.

"General, you know how valuable this gene is and how important the technology is to the human race. I need John Sheppard, the expedition needs John Sheppard"

Jack sighed.

"What can I do? He's already said he doesn't want to go"

Elizabeth sat forward.

"I know you can convince him Jack."

Jack sighed again and sat forward.

"You will be the death of me."

Elizabeth smiled, slightly embarrassed and looked down.

"Thank you."

Jack nodded and stood up.

"You owe me Elizabeth"

Elizabeth smiled again and turned to him.

"If he turns out to be a screw up I'll give whatever you want."

Jack smirked and Elizabeth began to get very red.

"Within reason"

She quickly added. Jack continued to smirk as he left the room. When he left the room Jack began to get very confused. He did not go there to flirt with her, but that's what he ended up doing, and call him crazy but she was responding to him. Jack shook his head, sure he thought Elizabeth was attractive, what man (or woman for that matter) in there right mind would think she was anything other than that, but she was against the military, at least she used to be.

Jack shook his head, this was getting him no way and it was pointless to think about it, she was going to another galaxy soon and there was nothing he could do about it.

Jack sighed before going off to find John.

**:End of Flashback: **

Jack picked his head off the bed and looked up at Elizabeth. He must have fallen asleep. He hadn't really got any rest since the Atlantis team stepped through the Stargate and it was beginning to catch up on him.

He squeezed Elizabeth's hand, which was still caught in his before bringing it up to his lips and kissing her palm.

"Come on, you are too strong to let those bastards beat you. Fight it"

It seemed that his pleas would never work, until he felt pressure on his hand. He looked up at Elizabeth and saw her eyes flicker open, just as they did John walked into the room.

"Elizabeth?"

He rushed over to her and took her other hand. Her voice was weak and croaky, almost impossible to make out but what she said was unmistakable.

"Jack?"

John froze when he heard her say the General's name. Jack saw him falter, saw the emotions come across his face. Anger, sadness, pain. There were all there.

Jack pulled his gaze from John deciding that he couldn't deal with this now. Instead he looked at the woman in the bed.

"Elizabeth I'm here. You are going to be okay. I promise"

Jack called for a medical team and the two of them were ushered out of the infirmary.

Jack looked at John, wondering what he was going to do, but he didn't do anything, instead he just walked away from the infirmary leaving Jack standing alone.

TBC…


	5. Chapter 5

Disclaimer: I don't own SG1 or Stargate Atlantis

Notes: Thanks for the reviews. 1 exam down 12 more to go and since it's the weekend I decided to write some more to this story.

* * *

Jack paced outside the infirmary as Cameron Mitchell turned into corridor and stood in front of him. 

"Any news?"

Jack stopped pacing and looked at Mitchell.

"Not since I got sent out of there."

Cameron nodded and sat down on one of the chairs outside the infirmary. Jack stopped pacing and sat down next to him. Jack clasped his hands together, closed his eyes and sighed.

Cameron Mitchell watched his CO, after hearing what Sam had said he had decided that he was wrong about the General and the Doctor, but seeing his friend like this was putting doubt in his mind. Maybe Sam was wrong, everyone knew that Sam and Jack were close but maybe he'd never told her that he had a fling with Weir.

In all honesty, Cameron was curious, he'd seen Jack worried before but this seemed like something different.

Cameron sighed and turned to Jack.

"General, can I ask you something?"

Jack opened his eyes and turned to Cameron and nodded, Cameron cleared his throat.

"Sir, I'm curious, you seem quite close to Dr Weir…" Jack nodded wondering were he was going with this "…did something happen between the two of you?"

Jack looked down at his hands, he didn't deny it, but he didn't confirm it either. He looked back up at Cameron.

"If you've kept up at all with politics you'll know she was against military action. Maybe still is,"

Cameron waited for him to continue but Jack stayed silent.

"Sir, I won't tell anyone, I'm guessing they don't know, but it seems you need to talk to someone."

Jack turned to Cameron and started to open in his mouth to begin to talk when the door to the infirmary opened. Jack stood up immediately.

"What's the news doc?"

The doctor walked over to Jack.

"She's doing better; she's awoke and has a full memory of what happened. Needless to say, she's in a lot of pain and is still having trouble breathing. We are going to keep a close eye on her."

Jack nodded and Cameron saw the relived look on his face.

"She's asking to see Colonel Sheppard"

Cameron saw Jack's face fall. Cameron had heard how Elizabeth had called for Jack when she woke up only raising his suspicion that something happened between them.

"He went back to his quarters to get some rest. I really don't want to disturb him."

The doctor nodded and turned back to the door when Jack stopped her.

"Can I see her? Make sure she's alright, so I can tell Sheppard when I see him."

The doctor nodded

"I don't see a problem there but only for five, ten minutes at the most."

Jack nodded and followed the doctor into the infirmary closing the door behind him.

He surveyed the room and saw Elizabeth on the same bed she'd been on hours before, propped up by pillows.

He slowly walked over to her, he saw she had her eyes closed and he wondered if she'd fallen back to sleep.

"Elizabeth?"

He said it so gently that when she didn't reply he thought she was asleep or hadn't heard. He was about to call her name again when her heard her call.

"John?"

Jack saw her open her eyes and smile at him, even if she was a little disappointed that John wasn't there.

"Jack? I guess it's true. We made it back to Earth."

Jack smiled and sat down next to her. He considered briefly whether he should hold her hand to show his support. Slowly he covered her hand with his. Elizabeth was slightly taken back but she turned her hand and gripped onto his.

"Thank you…for being here."

Jack smiled and held her hand tighter.

"Always"

Elizabeth smiled at him before looking down.

"Where's my team?"

Jack cleared his throat.

"Dr McKay, Teyla, Bates and the others are all on the base. You'll see them when you've gotten better."

Elizabeth nodded and turned to him.

"Where's Colonel Sheppard?"

John sighed

"He's in his quarters resting. I'll make sure he comes down to see you."

Elizabeth smiled in thanks while trying to suppress a yawn.

Jack saw her yawn and his chivalry kicked in.

"I should let you rest"

Jack stood up and slowly let go of Elizabeth's hand. He looked into her eyes.

"Get some rest honey"

He bent down automatically and kissed the top of her head.

"I'm glad you're okay"

He smiled at her and left the infirmary. He saw Cameron still waiting outside; Jack sighed and walked straight past him. Cameron waited for a moment before running to catch him up.

"Jack?"

Jack carried on walking.

"I've got some things to do Colonel."

Cameron followed Jack around the corridors and into his office. Jack sat his desk and turned to his computer. Cameron sat opposite him.

"Jack?"

Jack sighed and looked up at him. He looked over to the door to check it was closed before turning back to Cameron.

"Nobody knows about this Cameron and nobody can find out…"

**:Flashback: **

**SGC **(July 27th 2004)

It had been ten days since the Antarctica flirting and Jack had convinced himself he had got an hold on his emotions, that was until he saw Elizabeth leaning against the doorframe to his office.

"Dr Weir, what can I do for you?"

He gestured to the chair opposite him and Elizabeth walked into the office, closed the door and sat down. She smiled at Jack.

"I just wanted to thank you for your help on the whole Major Sheppard thing, I think he will be greatly beneficial to the expedition."

Jack smiled.

"You've already said that to me. Now what's the real reason you're here?"

Elizabeth smiled nervously and looked down at her hands.

"I wanted to thank you, not just about Sheppard, but about everything. When I first started here I was nervous and I'll admit I didn't think we would get along. I thought my position on the military would be the main cause of that but since I've been in Antarctica I have realised that the military do a lot of good in this world and I guess I have you to thank for helping me realise that."

Jack smiled and walked round to her Elizabeth stood up and faced him. They looked at each other, standing so close that they could feel each other's breath on their lips.

Their breathing began to get faster.

"I'm glad"

Jack slowly lowered his head and his lips touched Elizabeth's gently, giving her a chance to pull back but she didn't.

Elizabeth pressed her own lips onto Jack's.

Jack's hands made their way onto Elizabeth's hips as he pulled her closer to him.

Jack's brain was screaming, telling him it was insanity but his gut instinct was telling him that he wanted this.

All those years of wanting Sam, without success and he'd finally given in. Sam had Pete, whatever could have happened wouldn't anymore.

With Elizabeth, she was beautiful, successful, he respected her but sadly again nothing would happen.

Not only did she have a boyfriend but she was also leaving for the Pegasus galaxy within a month.

Jack's brain eventually won and he slowly pulled his lips away from hers. He kept his hands on her hips and finally noticed that her arms had worked their way around his neck.

Elizabeth slowly pulled her arms from around his neck and Jack took his hands off her waist.

"Um, best of luck out there"

What else could he say? He'd just come on to her. Just kissed her without any hesitation and she responded.

Elizabeth nodded.

"Thank you…sir"

Elizabeth quickly left the office.

**:End of Flashback:**

Cameron listened to Jack's every word.

"We eventually talked about it and agreed that we'd just forget about it, and we did. But…she…she just does something to me, something she doesn't mean to and it's something I can't resist."

Cameron nodded and sat forward.

"Do you feel something for her, or is it just lust?"

Jack looked at him. His face showed his confusion and how unsure he was.

"I…don't know."

TBC…


	6. Chapter 6

Disclaimer: I don't own Stargate Atlantis or SG1

Note: Uh oh, some of you don't like what I'm doing here with Jack/Elizabeth.  
I'll admit I was expecting some people not to like it, while others did, and even though I can't tell you what I have planned for this story I do hope you'll keep reading to find out. I do know how this fic will end. Sorry it's took a while to post but I'm doing my GCSEs at the moment and I'm really busy.

* * *

John sipped his third cup of Coffee as someone sat down in front of him. 

"Dr Jackson"

Daniel picked up his own Coffee and took a sip.

"I'm surprised, I thought you'd be at the infirmary seeing Elizabeth. I heard she'd woken up"

John shrugged and poured some more sugar into his cup.

"I know she's awoke. General O'Neill is with her. She wanted to talk to him."

Daniel nodded,

"So are you going to get over this jealous streak and be there for Elizabeth or are you going to keep acting like a kid who's just lost his favourite toy?"

Daniel took another sip out of his Coffee, he'd heard from one of the nurses that Elizabeth had called for Jack, she had also told him that John didn't seem to happy about it.

John looked up at him, sighed and lowered his head again

"What do you know about it?"

Daniel sighed and leant across the table.

"I know Elizabeth is a good person, it's pretty obvious you feel something for her, the chances of Jack and her _ever _working is like one in a million. I don't think you need to feel threatened. I also know Elizabeth has been asking for you"

John's head shot back up.

"She's been asking for me?"

Daniel nodded and John shot out of his seat and left the mess hall. Daniel smiled and took another sip out of his Coffee.

* * *

John arrived outside the infirmary and stopped. He paced for a little bit wondering what he could say to her. Would he ask her why she called for Jack? Would he want to know the answer? 

John finally decided that he'd let her take the conversation, he walked into the infirmary and saw Elizabeth, she was propped up by pillows and had her head resting on them. Never taking his eyes of her, he walked over to a doctor.

"Is it alright if I talk to her, just for a few minutes?"

The doctor was about to object until she realised who he was. The doctor smiled

"She's been asking for you."

John smirked and walked slowly over to Elizabeth's bed, he sat down, grabbed her hand and whispered

"Elizabeth?"

Elizabeth slowly opened her eyes, her vision was slightly distorted at first but she didn't need her eyesight to know who it was.

"John"

She smiled and John relaxed instantly. He slipped his fingers in-between hers. Her hand was warm, inviting and it felt so soft.

"How are you feeling?"

Elizabeth smiled and ran her thumb across the skin of his hand.

"The Morphine kicked in about 15 minutes ago."

John smiled and kissed her hand unconsciously, not that Elizabeth seemed to mind.

"How are you and the others?"

John looked up and smiled, typical Elizabeth was worried about the others when she was probably the worst injured.

"Most of us are okay, a few cuts and bruises. There's a few more serious injuries but they'll be fine"

Elizabeth nodded and looked down.

"How's Teyla?"

John could feel how she tensed when she asked that. John held her hand tighter.

"She'll be fine. I promise you, everything will work out."

Elizabeth nodded and John noticed a few tears fall from her eyes. John stood up and sat on the edge of the bed, cupping her cheek and making her look at him.

"Elizabeth, you did what you had to. Teyla will eventually understand."

Elizabeth nodded slowly; John smiled and kissed her forehead tenderly making sure to avoid her cuts and bruises.

Elizabeth breathed in his scent and it calmed her, Elizabeth wrapped her arms around him and John returned the gesture making sure not to hurt her.  
Elizabeth placed her uninjured cheek against his shoulder and closed her eyes. John ran his fingers delicately through her hair; they stayed like that for a few moments before somebody standing in the doorway cleared their thought.  
Elizabeth opened her eyes and smiled at who she saw.

"Rodney"

John pulled away from Elizabeth and looked round to see Rodney ginning madly, he walked over to them and held Elizabeth in a very delicate hug.

"I've just heard you were awake. I was so worried, we were all so worried."

Elizabeth smiled at Rodney's concern, he really had changed during the years, and he was so much like a brother to her.

"I'm fine. Are you okay?"

Rodney nodded and pulled away from Elizabeth grabbing her other hand and holding it tightly.

Elizabeth smiled at the two men.

"You certainty know how to make a girl feel loved"

The two men smiled at her before sitting down either side of her.

* * *

Jack hovered near the door of the infirmary as he watched Elizabeth interact with the two men who were obviously very important to her. 

He saw how her smile lit up the room whenever John said something and he saw the admiration that John had for Elizabeth. Admiration and maybe something else.

Jack took one last look at her before turning round and heading back up to his office.

* * *

Teyla sat on her bed, clutching a pillow to her chest. 

Elizabeth had survived and was awoke; she didn't know how she felt about that. She'd killed Aiden after all, but she'd did do it to save him.

Teyla's mind had been working overtime since her talk with Rodney; Teyla knew that Rodney and Elizabeth were good friends but she also knew that Rodney would not stick up for Elizabeth if she'd had done something wrong.

Teyla sighed and thought about all the time she'd been with Elizabeth. The friendship they shared was deep; it was obvious but would it be able to survive this?

Teyla stood up quickly and left her quarters, she walked around the corridors of the SGC, very aware of the Airman who was following her.

She kept walking until she reached the infirmary; she hovered outside for a few moments watching Elizabeth with Rodney and John. Now she was here she had forgot what she was going to say. What could she say to her? She thought of Elizabeth as a sister and now she hated her for what she had done. That's what she told herself, but what if Rodney and Colonel Sheppard were right. What if it was mercy?

Teyla leant against the wall and sighed before standing up straight and walking in to the infirmary.

* * *

Elizabeth's eyes fell onto the infirmary entrance as Teyla walked in. Their eyes locked for a moment before Elizabeth looked down. She couldn't stand to see the pain and the anger in Teyla's eyes. 

John looked round and saw Teyla approaching, his instinct was to stand up and tell her calmly that she should go away and cool down, but there was something in her eyes, which told him it wasn't necessary.

Instead, he moved and let Teyla stand next to Elizabeth's bed. Seeing Rodney was about to object John shook his head, telling him that it would be okay.

Teyla stood still for a moment before sitting down on the edge of Elizabeth's bed and taking her hand.

"You did what was necessary and what Aiden would have wanted"

Elizabeth nodded slowly, tears filling in her eyes. Teyla leant forward and lightly hugged her.

"I am sorry I could not be more forgiving earlier"

Elizabeth nodded

"I'm sorry as well."

Teyla pulled back from Elizabeth, placing her hand on Elizabeth's uninjured cheek.

"It does not matter now"

* * *

Several hours after returning from the infirmary for the second time, Jack sat at his desk trying to block out his emotions and feelings, but try as he might they were still there and they were growing stronger. Jack thought he'd figured it out when Elizabeth left for the first time, thought he'd pushed them away but they were in hiding and waiting for her return. On her return, they'd confused him more than ever. Making him re-think everything he knew. 

Jack sighed, he'd finally got round to informing the President that Elizabeth had woken up, the President, not being a patient man, had requested that she be debriefed the next day by the Joint Chiefs.

Jack sighed and stood up, switching off his computer and walking over to the door.

He left his office and began walking down to the infirmary. The SGC was mostly quiet apart from the night staff.

He walked into the infirmary, as his eyes drifted over the patients and settled on Elizabeth.

She was wrapped in the covers looking so peaceful and delicate. It hit him right in the heart to see her like that. He shook his head and turned to walk out of the infirmary when a small voice stopped him.

"General?"

Jack looked round and saw the person who had whispered in her sweet little voice. She was smiling at him, but still looked half-asleep.

Jack walked over to the bed and sat on the chair next to it.

"Hey, did I wake you up?"

Elizabeth shook her head.

"No, I was already awoke Today has been such a buzz, I can't sleep."

Jack nodded, his eyes staring at the spot where her hands lay, wondering, considering whether he should place his hand or top or remain a safe distance away.

"So, how are you feeling?"

They spoke in hushed tones, so not to disturb the other patients, most of who were sleeping.

"I'm okay"

Jack raised an eyebrow and sighed

"This is me Elizabeth. Now let's be honest"

Elizabeth sighed and looked away

"I'm sore, I can't breathe properly and the reason I'm not sleeping is because every time I close my eyes I see my people dieing."

Jack nodded

"Now that was honesty"

Elizabeth smiled and looked at him. Their eyes locked for a moment before Elizabeth spoke.

"Well don't go telling anyone. You have no idea how protective Rodney can be"

Jack chuckled and smirked

"You know, I've seen a new side to Rodney, I hate to admit it but I think I like it."

Elizabeth smiled and nodded her head

"Rodney had changed so much. Everyone's changed, but no one as much as Rodney. I know this sound weird, but I'm so proud of him."

Jack shook his head

"It's not weird…you know he cares about you a lot"

Elizabeth smiled shyly.

"He's become like a brother."

Jack nodded, suddenly sensing there was something they both avoiding.

Jack cleared his throat.

"Oh, the Joint Chiefs want to speak with you tomorrow…"

Elizabeth cut him off.

"Jack say it"

Jack looked at her in confusion but inside he knew what she meant.

"What do you mean?"

Elizabeth sighed and looked down

"Whatever you're tap-dancing around"

Jack looked away from her nervously.

"Do you want to talk about it?"

Elizabeth sighed and stared at him.

"Are things going to be weird between us if we don't?"

John shrugged, still not looking at her.

"Things could be weird either way. So do you want to talk about it?"

Elizabeth nodded

"I think we have to."

She sat up slowly; Jack quickly stood to help her. As she settled into a sitting position, Jack moved his hands up to her face and gently held her cheeks.

"When we first met I would never have thought you'd have such an impact on me. But you have."

Elizabeth slowly removed his hands from her cheeks and held them lightly in her lap.

"It has to stop Jack. It's been five years. We're different people now. We have different people in our lives."

Jack nodded slowly

"John?"

Elizabeth nodded slightly and Jack looked down.

"I figured as much"

Elizabeth lifted his chin with her finger and sighed

"Jack, it was one kiss, 5 years ago. Let it be"

Jack nodded and stood up; he began to walk to the door but looked back at her.

"If you hadn't left, would anything…"

Elizabeth shook her head sadly.

"I'm sorry Jack"

Jack nodded, smiled slightly and left the infirmary.

TBC…


	7. Chapter 7

Disclaimer: I don't own it. If I did, John, Elizabeth, Jack and Sam would all be locked up in a room together. Just for the heck of it.

Note: I know, it's been a while since I updated

**

* * *

Cheyenne Mountain Complex** (June 6th 2010)

Jack walked into the briefing room to find Elizabeth already there. She was neat, she was tidy and covering her bruises underneath liquid foundation.

She was in a black pants suit and white shirt and she looked seriously hot. Jack led himself away from that train of thought as he watched her, sitting between John and St Bates. Rodney, Zelenka and Teyla were all absent from the meeting as they were to undergo some more medical checks.

Elizabeth was calmly talking with the two men next to her, probably discussing the best course of action to take in this meeting.

When John noticed Jack and the Joint chiefs walk into the room, he shot a look to Bates and both men stood up. Elizabeth, who was still suffering from the effects of a punctured lung, remained seated. After all, she wasn't military.

The Joint Chiefs sat opposite the three members of the Atlantis crew and Jack took a seat at the head of the table. He turned to the Joint Chiefs

"Sir's, this is Dr Elizabeth Weir, head of the Atlantis expedition"

One of the Chiefs, a General Johnson looked at her.

"Dr Weir, thank you for agreeing to be debriefed so quickly. I understand you should be resting so we'll do this as quickly as possible"

Elizabeth nodded

"Thank you General. Although I must inform you there is a lot of material to cover"

Jack and John watched her in awe. This woman was injured, bruised and full of guilt and yet she could still take charge of a room. The confidence she showed in front of these men who could scare even the toughest Colonel was astounding.

General Johnson looked down at his notes than back up at Elizabeth.

"So Dr Weir, we have heard some of what happened from Major Sheppard and his team, but I understand there is a lot more, like what happened to Colonel Caldwell, Dr Beckett and the other members of the team."

Elizabeth nodded and cleared her throat before facing General Johnson.

**:Flashback:  
Atlantis **(June 3rd 2010)

Caldwell had lost track of how long he'd been sat with Elizabeth since the incident with Teyla.

He'd been doing his best to try and get her to talk but she was unresponsive.

Elizabeth knew Caldwell was doing his best to try to make things easier for her but she didn't deserve forgiveness or an easy ride. She'd killed a man, even if it was to save him, she still killed him

Slowly she felt a hand wrap itself around hers, holding it gently. Stroking a thumb across her knuckles. Soon a quiet voice accompanied the hand.

"You did what was best Elizabeth and what Ford would have wanted. Now do me a favour and stop blaming yourself Elizabeth"

Slowly she turned her head to face him and spoke in a soft tone.

"That still doesn't make it right Steven. We both know that"

Caldwell pulled his hand away from hers and wrapped his arm around her shoulders forcing her to let her head drop onto his shoulder.

"Elizabeth you have to stop punishing yourself. You are going to be no use to anybody. Do us all a favour and get some rest."

Elizabeth shook her head lifting it from his shoulder

"I can't"

Caldwell looked at her firmly

"Elizabeth, you need to rest. I wake you if anything happens."

Realising she was too tired to fight with him she slowly dropped her head onto his shoulder and closed her eyes.

John watched from across the lab as Elizabeth dropped her head onto Caldwell's shoulder and close her eyes. He couldn't help but feel a pang of jealousy that Caldwell was the one comforting her and not him. Slowly he shook his head and decided that it was not the time.

He sat there watching them for a few moments before Bates walked over and sat down next to him.

"How are you doing Sir?"

Bates had changed quite a lot; impending doom will do that to a person, although he still had a dislike for Teyla and the Athosians.

John turned round to face him and nodded.

"I'm fine"

Bates looked over at Elizabeth and Caldwell, sighing.

"For what it's worth, she did the right thing."

John nodded slowly

"I know. She did what I couldn't"

John looked down and shook his head.

"It's the waiting Bates. We are going to die, it'd be better if we all committed mass suicide. It'd be less painful."

Bates shook his head

"We'd never do that Sir. We have fought and fought, we will not let them beat us and we will not lead them back to Earth."

John nodded slowly.

"Lets' just hope we can keep the Wraith away otherwise nobody will be going home"

Bates was about to reply when McKay shouted

"I did it…I mean we did it."

John stood up and walked over to McKay was with his team, Elizabeth and Caldwell.

"We have managed to create a blast 10 percent more powerful then what we initially had."

Elizabeth smiled at Rodney weakly

"Well done Rodney, that plus the C-4 charges should ensure that the Wraith don't get this city in one piece"

Caldwell looked at Elizabeth and after she nodded at him, he took charge of the group.

"Okay, listen up. We have been going over the best way to get to the 'Gate. There are 50 of us…"

"…49, there are 49 of us left"

The interruption came from Teyla who had tears in her eyes. Caldwell saw Elizabeth look down sadly before continuing.

"…there are _50 _of us left, with such a high number going to the 'Gate in such a big group means that we're target practise if the Wraith spot us. This is how it's going to work. We are going to split into two teams of twenty-five, I'll lead one team, Colonel Sheppard will lead the other"

Caldwell quickly did a head count of the military personal in the room

"Even military on both teams."

With only 9 military personal plus Teyla they were short of experienced fighters, although after what these people had been through he figured they could handle it.

"Bates, you're with me. Stackhouse, Teyla, you're with Sheppard"

He split the rest of the personal, placing Elizabeth, Rodney, Radek, Simpson and a number of other scientists and three more military in his team. In John's team he placed the remaining personal including Carson, Kate and Kavanagh.

To be honest John had have been more comfortable if Elizabeth were with him, but he wasn't going to argue about it, they had a job to do.

**:End of flashback: **

Elizabeth stopped speaking as a sharp pain in her rips; she slowly picked up a glass of water and sipped in delicately.

Jack, John and Bates all looked at her worryingly. Bates was the first to speak

"Dr Weir are you alright"

Elizabeth nodded weakly,

"I'm fine"

John could see the pain clearly written across Elizabeth's face. He quickly turned to Jack who nodded before turning round to the Joint Chiefs

"I'd like to call a short recess, get Dr Weir checked out in the infirmary"

Elizabeth shook her head and started to protest but was interrupted by General Johnson.

"I think a break is what we all need right now, reconvene in one hour"

John, Bates and Jack stood up as the Joint Chiefs took their leave.

When the Joint Chiefs were gone, John slowly helped Elizabeth to stand up, noticing that she could no longer hide the pain in her rips.

He quickly placed one arm around her for support and Bates did the same before the slowly guided her down to the infirmary.

---

TBC…


	8. Chapter 8

Disclaimer: Not mine

Note: Sorry it's took me a while to get this posted. Thanks for the reviews.

* * *

Dr Lam carefully felt around Elizabeth's ribs, as she did Elizabeth winced in pain. Dr Lam looked at her with a slightly pissed expression. 

"How long have you been in pain?"

Elizabeth sighed for a moment before replying.

"A few hours"

John and Dr Lam both sighed at the same time. Dr Lam then shook her head and wrote something down in Elizabeth's notes.

"I told you to come see me if you were in pain."

John looked at Dr Lam concerned

"What's the problem?"

Lam sighed and looked sharply at Elizabeth before turning back to John.

"The lung that as been punctured was bleeding internally. We stopped the bleeding but the lung is very swollen. I told Dr Weir that if she was in any pain she had to come and see me so I could make sure that the bleeding hadn't started again, she didn't come to see me and the bleeding as started again"

John looked down at Elizabeth who was still laying on the bed and shook his head.

"I want Dr Weir to stay in the infirmary for at least the next few days so I can keep an eye on her"

Dr Lam's voice caused John to look back up at the doctor before nodding in agreement.

Elizabeth was about to protest when John stopped her.

"Don't argue. I'll sort out the Joint Chiefs"

Elizabeth dropped her head onto the pillow behind her and moaned. John smirked and lent down to kiss her forehead.

"I knew you'd see it my way"

Elizabeth lifted her head back up just in time to see Sam in the doorway. Sam cleared her throat and John looked round at her.

"Ma'am"

Even though Sam was the same rank as him, there was something that made him feel uneasy around her.

Sam nodded and walked over to the bed just as Dr Lam excused herself.

John suddenly got the feeling that there was something Sam wanted to talk to Elizabeth about in private so he quickly made up an excuse about having to see Jack and left the room.

Sam waited for John to leave before sitting down in a nearby chair. She smiled polity at Elizabeth before beginning.

"How are you feeling?"

Elizabeth nodded and smiled back. .

"I'll be fine"

Sam nodded

"A lot of people are worried about you. Rodney was a wreck"

Elizabeth answered, a little sharply.

"Well surprising Rodney does have feelings."

Sam was slightly taken back

"I was just saying he's changed a lot in 5 years"

Elizabeth shrugged slightly

"You never really knew him Colonel. Rodney...he is one of the best members I had on my expedition"

Sam nodded, everyone she had talked to that had been on the expedition had said that, despite being a little pig-headed at times, Rodney had saved their asses more than once and had become a friend and role model to a lot of them.

Sam sighed and glanced around the infirmary before looking back at Elizabeth.

"I have to ask, I'm curious...are you and Colonel Sheppard..."

Elizabeth shook her head

"No"

It was true, they hadn't really talked about if anything had changed in their relationship but things he did seem different since they had been back on Earth. In truth things between them had been developing for a while.

Sam nodded.

"Will it?"

Elizabeth thought for a moment before answering.

"I'd rather not say. It's personal"

Sam nodded in understanding.

"Look, Elizabeth I know I was a bitch to you back when you were in command of the SGC, but I believe in leaving the past in the past. We are properly going to be working with each other and I don't want it to be weird between us. I'm not saying we should be best friends, but I just think we should try to be more civilized to each other."

Elizabeth laid still for a moment before responding.

"I never really understood why you disliked me in the first place, I don't know if it was because I was replacing Hammond or something else, but I don't like being in that position so if you want to give it a shot with us being civilized, I will try."

Sam nodded

"I'm glad"

A part of Sam did want her of Elizabeth to try to get along, but another part of her, a larger part, wanted to know what was going on with Jack and she knew Elizabeth held the answer to that.

* * *

John knocked on the door to Jacks office. After receiving a slightly annoyed, 'what?' he walked in. 

Jack looked up at him and gestured to a seat.

"How is Dr Weir?"

John smiled and leant back slightly.

"The Doc chewed her out. Internal bleeding from the ruptured lung. Dr Lam is keeping her in for observation"

Jack nodded, looking down at some papers before looking back up at John.

"John, I'm curious, what are you going to do after all the debriefings and meetings?"

John sighed.

"I haven't really thought about it. I'd like to stay in close contact with Elizabeth and McKay but other then that, I don't know."

Jack nodded

"I have a proposition. We've been forming some new teams lately. I would like you, McKay, Bates and Teyla to be one of those teams. From what I've heard you four would fit together perfectly as a team"

John sighed

"Bates and Teyla have issues with each other. I don't know if putting them on the same team would work."

Jack nodded and leant back.

"What do you suggest?"

"Bates is capable of leading his own team. He did in Atlantis and he did a fine job. I would like to recommend that he gets his own team, if he wants one."

Jack nodded

"I'll recommend it. But you still need another member"

John nodded

"Major Lorne. I trust him with my life."

Jack nodded.

"Well, if you all decide to stay in the programme, you have your team"

John nodded and shifted in his chair trying to get comfortable.

"Do you think Elizabeth will go back to the government?"

Jack took a sip of water before answering,

"A lot of people actually thought she was dead to begin with. That damn boyfriend of hers didn't help"

John sat up.

"Simon right? What did he say?"

Jack sighed

"He mentioned to some undercover reporter that she was doing some work for the military. He didn't know that she was a reporter but it didn't half cause some problems. Rumours saying that the military put a hit out on her started spreading. It eventually stopped after it was reported that she was working with the military in the Far-East."

John nodded and Jack continued

"So in answer to your question I don't know. I would like her to stay in the SGC, I think she would be greatly beneficial."

John nodded.

"I'll guess I'll have to have a talk with her."

**Cheyenne Mountain Complex **(June 8th 2010)

It had been five days since the Atlantis team had come through the Stargate and the President was getting edgy. He wanted answers and they only person he would except them from was Elizabeth. Despite the fact she should be resting, so here she was again, in the briefing room sitting in front of the Joint Chiefs going over the events of the last few days over and over again.

"Again, Dr Weir tell us what happened when you split into groups"

Elizabeth sighed

"I can only speak for what happened in my own group"

**Flashback**

**Atlantis (**June 3rd 2010)

After the groups split up Caldwell took his group to the west of the city where they would circle back round to the control room and John's team went to the east where they would do the same. Elizabeth felt shaky with the P-90 in her hands but she knew she couldn't let it show. So she quietly followed Caldwell as he led the group around the darkened and destroyed city.

Their main objective was to get out of the city as quickly as possible but when the Wraith came round the corner, it was obvious that was not going to happen.

The fight started so quickly it was impossible to see what was happening. To survey it all and try and protect everyone.

Elizabeth was shooting at a Wraith when she saw another go up behind Bates', quickly she changed her position and shot the wraith through with all she had before it fell down. Bates' turned back to her and was about to smile in thanks when another Wraith flung Elizabeth across the room. Elizabeth head flung back in pain as her rips felt like they would pop out of her skin. Bates' ran up to her and quickly lifted her, placing one of his arms around her to steady her.

"Can you walk?"

Elizabeth shook her head. The combined pain in her ankle and rips was killing her. Quickly Bates' placed a P-90 in her hands and picked up another for himself. He grabbed the rest of the group; they were in such a rush that she didn't even realised that Caldwell wasn't with them. After about five minutes she looked around the group. Rodney was still there, but Simpson was missing, so was Dr Kim and a few others, that's when she realised Caldwell wasn't there. She turned to Bates' was still had one arm around her.

"Bates', where's Caldwell?"

Bates' cringed and sighed

"He was caught up with a Wraith. He didn't make it"

Elizabeth stopped and thought she was going to be sick

"Come one, Doc. We've got to keep moving"

Elizabeth nodded and carried on walking.

* * *

After another twenty minutes, they finally met up with John's team near the 'Gate room. Not surprisingly, there were people missing from that group but Elizabeth noticed two main people missing immediately. 

"Where's Carson and Kate?"

John sighed

"They didn't make it, neither did Kavanagh or Stackhouse"

Elizabeth heard a gasp and turned round to see Rodney who looked like he was about to throw up. Slowly Elizabeth untangled herself from Bates' and turned to Rodney. She then wrapped her arms around him and hugged him tightly, ignoring the pain in her ribs. Rodney buried his head into her neck, she could feel the wetness on his cheeks as it poured onto her neck.

John watched as Rodney broke down in Elizabeth's arms. He wished he could let them have a few more moments but he knew they had to keep moving.

"We have to keep going?"

Rodney pulled away from Elizabeth and wrapped one arm around her to hold her upright while Bates' wrapped another arm around her. John looked out at the rest of the personal

"Where's Caldwell?"

Elizabeth's voice cracked

"He didn't make it"

John slowly nodded and led the group.

* * *

As the group neared the control room they became more weary. They knew that the Wraith had properly figured out their game plan and were waiting for them. They snuck into the control room. John and Rodney went up to the control room and started dismantling what they didn't couldn't let the Wraith get their hands on. When that was done, John sent Rodney down to the group as he dialled the 'Gate. 

As the Stargate activated and the IDC was sent through, John ordered the group to go through. Rodney, Bates', Elizabeth and John were the only ones left. All four had the detonators which would blow up the city.

One by one they took out the detonators.

"After 3, hit the button, then run like hell"

The group nodded as Elizabeth mentally timed the self-destruct

_15, 14, 13, 12_

"1...2...3"

_11, 10, 9_

All three of them hit the detonators, Rodney then ran through the 'Gate while Bates and John wrapped their arms around Elizabeth

_8, 7, 6, 5_

They then rushed through the Stargate before the self-destruct destroyed the rest of the city

_4, 3, 2_

They arrived on the other side of the Gate and she was sure she could hear as the self-destruct went off just as John ordered the iris to be closed

_1, 0_

**End of flashback**

"From what I understand, Colonel Sheppard's group got into a fire fight as well, that's why they lost some members."

General Johnson sat forward.

"Thank you for co-operation Dr Weir. I know talking about it cannot be easy."

Elizabeth shook her head

"Talking about it is easy, especially when you've lived through it."

General Johnson nodded.

"I understand Dr Weir"

**Cheyenne Mountain Complex **(June 18th 2010)

Elizabeth looked around her new office at the SGC. She was surprised Jack had sorted out a job for her and her team so quickly. She was grateful for that. She just wanted to get back into the swing of things, to try and forget what had happened.

There was a knock at the door, Elizabeth turned round and saw John standing there. A typical smirk on his face.

"Hey, getting all settled in"

Elizabeth nodded.

"I'm actually surprised he managed to get it sorted out so quickly"

John smiled and sat down in Elizabeth's chair.

"He's been planning this since we came back."

Elizabeth nodded

"He still works quickly"

John nodded and shifted to make room in the chair for Elizabeth to sit down. Elizabeth shook her head but John grabbed her hands and dragged her down on to his lap. He circled an arm around her waist and Elizabeth looked back at him, resting her head on his.

"This is inappropriate"

John shrugged.

"I'm not your subordinate anymore and you weren't complaining for the last 5 days"

Elizabeth laughed slightly and smiled. The past 10 days they had been working on what was going on between them, finally five days later they had decided there was no point in resisting what they wanted and they had spent the time getting to know each other, among other things.

John placed his hand on her cheek and was about to kiss her when they heard someone in the doorway clear their throat. Elizabeth turned round to see Jack standing there. Slightly embarrassed she stood up and looked at Jack.

"General"

Jack nodded

"Doctor, Colonel"

John stood up and faced Jack.

"Sir"

Jack looked around the room

"Just checking to see that you are settling in alright"

Elizabeth nodded

"Yep, everything's fine."

Jack nodded.

"I'll leave you to it then"

Jack turned round and left her office. When he was outside he leant against the wall closing his eyes.

"Stop it Jack. Leave it be"

TBC…


	9. Chapter 9

Disclaimer: Don't own the boys and girls at Atlantis or SG1

_

* * *

The cold wind blew through the trees, swaying them and causing the leaves to fall slowly from them. Elizabeth lent hard against one of the trees and caught her breath she could hear the sound of feet rushing towards her. Sighing she stood up straight and unstrapped her gun from her hip strap. _

_Suddenly she felt a hand grab hers._

"_Doc, we've got to keep moving"_

_Elizabeth turned and saw Aiden. Slowly she nodded an Aiden pulled her along by her hand. _

_They kept walking in silence, eventually they lost track of time and Aiden turned to her and lent against the tree behind him. _

"_They must be only about an hour behind us, if their on foot."_

_Elizabeth nodded_

"_I know."_

_Slowly she lifted up her gun to her waist before looking back at Aiden._

"_How's your leg?"_

_Aiden looked down at his leg, which had a deep cut down it. _

"_It'll be fine"_

_Elizabeth nodded_

"_It's slowing us down, Aiden"_

_Aiden looked at her, annoyed_

"_I know. I'm trying"_

_Elizabeth nodded_

"_I know that Aiden, but I can't afford to let you slow us down."_

_Elizabeth raised her gun and pointed it at Aiden._

_Aiden shifted nervously backwards staring at the gun in her hand._

"_Please, please don't"_

_Aiden continued to beg for his life as Elizabeth kept the gun raised at him. _

_Tears fell down Elizabeth's face._

"_I'm sorry Aiden"_

_Elizabeth squeezed the trigger and a shot rang out through the woods._

* * *

Elizabeth sat bolt up in bed. Sweat dripping down her body as the dream continued to play out in her head. The coldness and harshness scared her greatly. Shaking she reached over to her bedside table and picked up the glass of water sitting there. She brought it to her lips and gulped it down. Elizabeth placed the glass back down and winced as she felt a sharp pain in her lung. She began to breathe heavily and wheezing. Her wheezing became loud and disturbed the man next to her. 

John sat up next to her, rubbed her back gently and kissed the side of her head.

"Take deep breaths"

Elizabeth continued to wheeze, pain invading her lungs. John reached over to her side of her bed and picked her Inhaler. He'd seen her have asthma attacks before on Atlantis but he'd never seen her have one this bad before. The first time she'd had an attack on Atlantis was after Peter's death, he'd found her in her room, sitting on the floor, wheezing, he hadn't even known she was asthmatic.

He had eventually found her Inhaler and calmed her down.

He handed her the Inhaler and she sprayed the contents into her mouth and breathed them in deeply. She shut her eyes and laid her head back on the wall behind her.

John placed his arm around her and kissed the side of her head again.

"Are you okay?"

Elizabeth nodded and placed her head on his shoulder. John slipped his hand though her hair. Her breathing began to steady and finally the wheezing stopped. John turned to look at her and could see tears rolling down her face. John wiped the tears from her face with his thumb.

"Wanna talk about it?"

Elizabeth shook her head and snuggled back down into the bed cover and held on to John. John sighed and shifted down next to her and held her tightly.

**

* * *

Elizabeth Weir's Home (July 1st 2010)**

John woke up and was aware that Elizabeth's warm body was not laying next to him. Opening his eyes, he looked around the room and saw that she wasn't there. Sighing John got out of the bed and pulled on a t-shirt as the unusual cold registered over his shirtless body. Slipping out of the room he walked down the stairs and into Elizabeth's kitchen were he could smell the freshly brewed coffee filling the room. Elizabeth was sat in the living room staring at the blank TV screen sipping her coffee. John took a mug out of the cupboard and poured himself a coffee before heading over to where Elizabeth was and sitting next to her, placing a hand lightly around her shoulder.

"How are you this morning?"

Elizabeth's eyes stayed on the TV screen and she answered him in a way that made him think she was daydreaming.

"I'm fine"

John nodded and lightly kissed the side of her head.

"Sure you don't wanna talk about it?"

For the first time that morning Elizabeth looked at him

"I'm fine."

John nodded and they sat there in silence for a few moments. John was looking at Elizabeth and registering how broken she seemed. Her voice, the way she looked, none of it seemed right.

"Look, I'm gonna take a shower and get changed"

Elizabeth stood up, placed her coffee on the table in front of them and walked out of the living room and up the stairs to the bathroom. John sighed and switched on the TV hoping to find something to take his mind off his worry for Elizabeth.

**

* * *

Cheyenne Mountain Complex**

John walked into the SGC briefing room and smiled as he saw his friends. It had taken a couple of weeks since Jack had offered him command of a team, to sort everything out but today was their first mission briefing. John walked over to Major Lorne, Teyla and Rodney and smiled at them.

"Hey"

Teyla smiled and nodded

"Colonel Sheppard, it is good to see you again"

John nodded and stepped forward to hug her lightly. He knew she was still hurting over Ford but lately he'd seen a change in her, there was something he couldn't quite put his finger on.

Next he turned to Lorne and giving in to the urge they gave each other a quick hug.

"Sorted everything out?"

Lorne nodded

"It's all sorted"

Lorne had been having some problems finding an apartment and getting his girlfriend to talk to him again after he'd left for Atlantis but things seemed to be going well.

John turned to Rodney.

"McKay"

Rodney

"Sheppard"

The two shared no looks or feelings towards each other causing Teyla and Lorne to share an amused look.

"How's Elizabeth? I haven't seen her lately"

John nodded

"She's okay, she's been really busy"

Rodney nodded

"Good, glad she's okay"

Teyla smiled and turned to John's

"Colonel, will you let Elizabeth know that once I have sorted out an..."She turned to McKay and he mouthed the word 'Apartment' at her "...apartment, I would love to have the two of you round for a meal"

John nodded

"I'll let her know."

Teyla gave him another smile and the group continued to catch up until SG1 and Jack walked into the room.

John saluted Jack respectfully and Jack saluted back.

SG1 sat down on one side of the table and John's team, which had been designated SG15, sat down on the other side.

* * *

A few hours later the briefing had finished. It had been about a mission to a heavily populated Goa'uld planet. The planet also held an ancient weapon which, rumour had it, could only be moved once activated by someone with the ATA gene, that was where John came in. The planet was not accessible by Stargate so the team would have to go by ship to the planet, get the weapon and then get back to Earth. The plan was to 'Gate to a nearby planet and then go the rest of the way by cargo ship. The mission would be about a week long and John already had problems with that. His main problem was leaving Elizabeth for a week. Despite what she said, she wasn't okay, there was something going on with her and he needed to know. 

John was broke out of his musing when Jack placed his hand on his shoulder

"John"

John looked up at him and then around the table.

"Oh, we're finished. I didn't realise"

Jack nodded.

"Yep, we're done"

John nodded, stood up but Jack stopped him before he could leave the room.

"What's the problem Colonel?"

John turned to him

"Nothing Sir"

Jack nodded and walked over to him.

"Don't make me order you to tell me"

John sighed

"It's Elizabeth"

Jack sighed and led John into his office.

"It's always a woman. Sit down, tell me what's wrong"

Jack was genuinely concerned, John was his friend, so was Elizabeth. It worried him if something was wrong with one of them.

John sat down opposite Jack and sighed.

"The last few nights she's been waking up, terrified. It's obviously nightmares but last night...it was the worst I've seen her. She was so terrified she had an asthma attack. She won't talk to me about it. She won't tell me what the problem is."

Jack nodded.

"She most likely doesn't want to burden you before this mission."

John sighed

"Will you keep an eye on her while I'm gone. It's just...I'm worried"

Jack nodded

"I'll look after her"

John nodded, stood up and left Jack's office.

* * *

Elizabeth rubbed her hand across her eyes and suppressed a yawn as she sat in her office and went over a recent treaty with a race of people SG3 had come into contact with. She went over the treaty changing paragraphs and highlighting important sections with a yellow highlighter. She was so immersed in her work that she didn't even realise the door open and John standing in front of her desk until he spoke. 

"You might want to change that bottom paragraph; it doesn't quite flow at the moment"

Elizabeth looked up at him.

"I haven't got to that part yet"

She looked back down at the treaty and John thought she forgotten about him until she spoke again.

"So, how did the briefing go?"

John shrugged and sat down

"Okay, the mission is going to be about a week long"

Elizabeth nodded and looked up at him.

"Be careful out there"

John smiled and grabbed her hand

"You know I will."

Elizabeth squeezed his hand tightly

"Come back to me"

She still didn't look up at him but kept hold of his hand as she highlighted another section of the treaty.

TBC...


	10. Chapter 10

Disclaimer: I don't own SG1, Atlantis, The Simpsons or The X-Files 

Spoilers: Season 2 X-Files, Up to and including seasons 9 and 2 SG1 and Atlantis

**

* * *

Cargo Ship **(July 5th 2010)

It had been only 2 days since SG1 and SG15 had left for their mission to secure the Ancient weapon and John was already worrying about Elizabeth. At the moment he was sat next to Colonel Cameron Mitchell playing noughts and crosses with him.

John smirked in triumph and placed another cross in the table in between two others.

"I win"

Cameron sighed and placed then pen he had in his hand down on the floor.

"Unbelievable, you've won every game."

John just smirked and drew another table.

"It's called practise Cameron, that and the fact Elizabeth taught me how to play this game to win everytime"

Cameron sighed and picked up the pen and placed a circle in one of the squares.

"I'm fairly certain that you're girlfriend teaching you how to win all the time is a form of cheating."

John just continued to smirk as he won another game. Cameron sighed.

"I'm not playing anymore, this is not fair"

John just smirked again.

"Can't take a loss Cameron?"

Cameron glared at him as Sam walked over to him. The two men looked over at her.

"Sam, what's the problem?"

"Sheppard can you come help me in the engine room?"

John nodded and turned to Cameron

"Practise, Teyla doesn't really know how to play; you might stand a chance against her"

John followed Sam quickly before he could be hit on the head by the pen that Cameron threw at him.

Once they were in the engine room Sam pulled out one of the hyperspeed panels and started moving around crystals.

"So what's the problem?"

Sam, still moving the crystals sighed.

"There was some resistance when we jumped into Hyperspeed after our last stop. It should be fine"

John nodded

"What do you want me to do?"

Sam motioned to the Sub-light engine panels.

"Check the sub-light crystals. I want to check nothings burnt out"

John nodded and headed over to the sub-light panel. He pulled out the panel, observed the crystals, and checked them out.

As they continued to check the crystals, Sam spoke.

"How's Elizabeth?"

John looked up at her, wondering, for a second, why she was so bothered. The two of them had never seen eye-to-eye but then her remembered Elizabeth telling him something about them calling a truce.

"She's doing okay. Most of her wounds are healed"

Sam looked over at him

"Physical wounds heal faster then emotional ones"

John looked up at her curiously.

"What do you mean?"

Sam looked back down at the crystals.

"The first person she's ever killed turned out to be one of her closest friends. It's going to screw her up"

John walked round to her

"Look, I know you don't like her..."

Sam cut him off

"John, this isn't a crusade against Elizabeth, this is a warning for you. She'll hurt you John"

John shook his head in disbelief

"You don't know her, she wouldn't do anything to hurt me"

Sam nodded

"Maybe not intentionally, but just be careful. I don't want to see anyone get hurt"

John sighed and walked over to her.

"Look, don't dance around it, I'm not stupid, if you are trying to tell me something happened between her and Jack I know. She told me"

Sam looked up at him shocked

"What? Something _did _happen between them?"

John nodded

"Before the expedition left for Atlantis. It was just a kiss and there's nothing between them now. Now that you know I would appreciate it if you didn't use her for your own agenda."

"When did she tell you?"

John sighed

"Just after we settled into the SGC. She wanted me to know, she didn't any secrets between us"

Sam took a deep breath and looked at John.

"Why do you trust her?"

John shook his head and sighed

"You really don't know her Sam"

With that, he left Sam alone in the engine room.

**

* * *

Cheyenne Mountain Complex**

Elizabeth sat in her office going over a mission report about why an alliance with a race of people on P4X-546 had ended with two of their people recovering in the infirmary with bullet holes in their stomachs.

Elizabeth sighed when she heard a knock at her office door. Reluctantly she answered.

"Come in"

The door swung open and Jack walked into her office smiling.

"What you up to?"

Elizabeth looked up at him and smiled at his attempts to relax.

"I'm going through the mission report to see if there is any chance in saving our alliance with the people on P4X-546."

Jack nodded and sat down opposite her.

"Any chance?"

Elizabeth shook her head

"I don't think so. They may have injured two of our people but we killed a lot more of there's"

Jack sighed and sat back. He looked at Elizabeth and noticed how stressed and tired she seemed.

"How long is it since you slept?"

Elizabeth looked up at him and sighed

"Jack..."

"Elizabeth..."

Elizabeth sighed and dropped her head onto the back of her chair.

"I'm just having a bit of trouble sleeping. That's all"

Jack nodded

"Have you seen Carolyn about it?"

Elizabeth shook her head

"The last thing I need at the minute is Lam pumping me full of sleeping pills"

Jack nodded

"Okay, but if you need to talk to anyone, my door is always open"

Elizabeth nodded

"Okay"

Jack stood up and walked to the door, stopping when he got there.

"When was the last time you ate?"

Elizabeth looked up at him

"I'm fine"

Jack sighed and left her office

**

* * *

Elizabeth Weir's Home **

Elizabeth sat on her sofa drinking a glass of wine. She flipped through the channels on the TV trying to find something to watch that didn't revolve around fighting, war, or anything intellectual, instead she turned it on to 'The Simpsons'. She crossed her legs, picked up the bottle of wine, which sat on the table and poured some into the glass she held before settling down for a night of mindless cartoon comedy. She was only about 5 minutes into the episode when there was a knock at the door. Sighing she placed the wine down on the table and went to the door.

She opened the door and saw Jack stood there with a very large pizza and a smirk on his face.

"Jack?"

Elizabeth glared at him, pissed, but Jack just smiled

"I thought you could use the company. Plus I don't want to eat this whole pizza to myself"

Elizabeth smiled, knowing that he was just trying to be sweet. She moved away from the door and gestured him in.

"Come in"

Jack smiled, walked past her and down into the living room, smiling at what was on the TV while Elizabeth headed into the kitchen and grabbed two plates and a 6 pack of beer knowing how much Jack could drink.

She headed back into the living room and sat on the sofa next to Jack placing the plates and beers down on the table in front of her.

"This Simpsons is a classic."

Elizabeth nodded, a wry smile on her face as she picked up her glass of wine and took a sip.

Jack leant forward and grabbed a slice of pizza, placing it on one of the plates and then grabbed another piece putting it on the second plate and handing it to Elizabeth. Elizabeth smiled and took the plate. Jack grabbed his own plate and took a can of beer before settling back into the sofa.

* * *

Jack turned to his side to see Elizabeth still sleeping peacefully next to him. After watching 'The Simpsons' and eating pizza, Jack had put on a film. It hadn't taken long for Elizabeth to fall asleep next to him. Jack guessed that she hadn't slept much lately so he decided to leave her while he watched the end of his film. Slowly during the course of her sleep Elizabeth had worked her way over to him and ended up with her end resting on his shoulder with his arm around her. Jack knew that Elizabeth must be used to always having John at her side to cuddle up to so he just let her stay there. 

Jack took a long swig from the can of beer, which was sat on his leg as he flipped through the channels looking for something to watch. He came across an episode of 'The X-Files' and decided to stick with this. Besides, Jack though Scully was hot, although to Jack's dismay the episode being played was one of the season 2 episodes without her in.

Jack continued to watch the TV until he felt one of Elizabeth's hands which was placed on his chest screw into a ball. He looked down. She looked terrified and was muttering 'no' over and over again. Jack brushed back her hair and tried to came her down.

"Elizabeth. Elizabeth wake up, it's not real, you're dreaming"

Elizabeth continued to fight against him unconsciously as she slept. Jack held her arms and shook her gently

"Elizabeth"

Elizabeth's eyes opened wide and she stared at Jack. Getting to her feet and finding her balance Elizabeth walked into the kitchen with Jack following.

"Elizabeth talk to me. What the hell was that?"

Elizabeth sighed

"A nightmare, it was just a nightmare"

Jack nodded

"That seemed like the mother of all nightmares. What was it about?"

Elizabeth started to tell him that it didn't matter but Jack looked at her sharply.

"It was about Aiden. About 4 years ago we were on a mission. Aiden and I got separated from the team when the natives turned on us. Aiden was injured; it was bad. He could barely walk. He was so worried about me being captured, he told me to leave and to go on alone. I didn't, I couldn't. I told him I wouldn't leave him to get captured. That's when he told me to kill him. He gave me his side arms. He told me it would be quick and painless, I told him I wouldn't do it. He got angry with me, told me I'd be captured as well if I didn't do it. I told him I wouldn't leave him behind and I wouldn't kill him. We were lucky. John found us before the natives could. In the nightmare Aiden is injured, his leg isn't as bad, he can still walk on it. We get to a forest. The natives are only a hour or so behind us on foot. Aiden's injury is slowing us down but he's trying to get me to safety. I shoot him. I shoot and kill him without a second thought."

Tears began to fall from Elizabeth's eyes. Jack walked over to her, wrapping his arms around her. She rested her head on his shoulder.

"I killed Aiden and I'm just living my life normally. I murdered a man and I haven't been punished at all."

"Is this what you've been keeping from John?"

Elizabeth nodded

"I killed his best friend. He doesn't need reminding of that"

Jack nodded and pulled away from her.

"Elizabeth I want you to see the on base Psychologist"

Elizabeth shook her head and Jack sighed

"I will make it an official request"

Elizabeth stepped back from him and lent against the table.

Jack walked over to her and placed his hand on her cheek. For a moment, she thought he would kiss her. He thought he was going to kiss her but instead he grabbed her hand.

"Come on"

He squeezed her hand and led her back into the living room.

**

* * *

Cargo Ship **

Cameron threw a pen across the room as he lost another game of noughts and crosses.

From where she sat Teyla could see the anger written on the pilots' face. She smiled and shook her head deciding that men from Earth were most interesting and weird. Standing up she walked over to where Rodney was sat.

"May I sit with you?"

Rodney nodded and Teyla sat next to him.

"You don't have to ask"

Teyla nodded

"You seemed busy"

She nodded to the book which sat in his lap but Rodney shrugged

"I've read it before."

Teyla nodded and smiled

"I do believe Colonel Mitchell may hurt Colonel Sheppard."

Rodney looked over to where the two men where sat.

"They've been playing that for hours."

Teyla nodded

"I was relieved when Colonel Sheppard came back and played with him. I was beginning to get uncomfortable with Colonel Mitchell's anger"

Rodney sighed

"They are just childish"

Teyla laughed slightly

"And you are not?"

Rodney glared at her

"I'll have you know that I am not childish. I am very mature"

Teyla nodded and shifted closer to him.

"I like you being Childish, so long as it is not in the middle of a mission"

Rodney nodded and grasped her hand which had made it's way onto his leg.

* * *

Daniel crossed his arms across his chest as he watched Teyla and Rodney. They seemed close. Granted, they had spent a lot of time with each other since coming back to Earth. He continued to watch them as they talked quietly. If what he thought was happening was happening, well then it would be a big shock. To everyone. 

TBC...


	11. Chapter 11

Disclaimer: I don't own Stargate Atlantis or SG1

Note: Not beta'd so all mistakes are my own. **Also as it appears that this needs to be stated. This Fic is AU, it takes place years into the future. Things have changed, people have change. Just because somebody wouldn't have done something back during season 2 Atlantis doesn't mean they won't do it 5 years into the future. **  
Pairing: John/Liz, Jack/Sam tension, Jack/Liz (Not quite sure in what context yet)  
Spoilers: To be safe up to and including season 2 Atlantis and season 9 SG1

**Cheyenne Mountain Complex **(July 7th 2010)

Elizabeth sat opposite the SGC Psychologist. She'd kept her promise to Jack and he hadn't even had to drag her there, though he swore he would if she didn't go.

Elizabeth slid her fingers around the rim of the glass she was drinking from. The Psychologist had just asked Elizabeth a question which she didn't know the answer to. She wasn't sure she wasn't sure she wanted to know.

"Elizabeth?"

Elizabeth's head snapped up.

"Sorry...what did you say?"

The Psychologist smiled at Elizabeth and asked the question again.

"I asked you how you felt about Aiden's death"

Elizabeth stared at the glass in her hand

"Numb. Angry. Ashamed, partially ashamed. He was a young man, had his whole life ahead of him. He shouldn't have died the way he did"

The psychologist nodded and wrote something down

"And what was your relationship with Aiden?"

"He was…he was my friend. One of my best friends. I cared for him so much. I loved him so much"

**Cheyenne Mountain Complex **(July 14th 2010)

"Any news Jack?"

Jack looked up to see Elizabeth standing in the doorway. Jack sighed and shook his head

"I'm sorry Elizabeth. Nobody as seen them. The Tok'ra have sent out ships to positions where they could be but there's nothing"

Elizabeth nodded slowly.

SG1 and SG15 were two days overdue. Nobody had heard from them. Elizabeth was worried, she didn't know what she'd do if something had happened to them.

Elizabeth sat down and faced Jack.

"The engines could have just burnt out, right?"

Jack knew she was fishing for a explanation so he nodded slowly

"Of course. Happens all the time"

Elizabeth nodded slowly

"Let me know if you hear anything"

Jack nodded and watched as Elizabeth stood up and walked to the door, Jack's voice stopped her

"Have you eaten yet?"

Elizabeth shook her head and faced him

"No"

Jack nodded and stood up, walking around his desk towards her

"Come on, let's go get some lunch"

Elizabeth nodded. Jack opened the door and Elizabeth stepped out, followed by Jack.

**Goa'uld Prison camp **

John was pushed down into the cell by two Jaffa. His rips protesting as he hit the hard floor.

"Jeez, can't you be gentle?"

That earned up another hit across the head with a staff weapon before the locked up the cell and walked away.

Teyla slid over to John and helped him to sit up

"John are you okay?"

John nodded slowly and rested his head against Teyla's shoulder

"Jeez, my head is fucked"

Teyla couldn't help but laugh slightly. She placed her arm around him.

"I am sure you'll be fine."

John closed his eyes for a moment before opening them and looking out across the other people in the room.

"Where's Cameron?"

Teyla sighed slowly

"He…he was taken away a few hours ago"

John nodded slowly and closed his eyes again. Tears began to fall from his eyes, tears he quickly pushed back.

His thoughts drifted to Elizabeth. He knew she'd be going stir crazy. He pictured her pacing up and down the corridors of the SGC waiting for news on them.

"Teyla?"

Teyla twisted her head and looked at him.

"What is it?"

John swallowed hard and sighed

"Teyla…I know I shouldn't be thinking this way but if I don't make it out of this…"

"…John don't talk like this"

John shook his head and took his head from Teyla's shoulder and faced her.

"Just let me say this Teyla…just in case…I just want you to tell Elizabeth…just tell her that…I love her and…and not to…just tell her I love her"

Teyla nodded slowly

"We will get out of this John"

John nodded slowly and placed his head back on Teyla's shoulder

"Just make sure she knows. Please honey"

Teyla nodded slowly

"I will tell her"

**Elizabeth Weir's Home** (August 31th 2010)

Elizabeth clumsily placed her glass on wine on the table, spilling some of the contents on to the floor, not that she realised.

She leaned back into the sofa and sighed.

It had been over a month. John and the team had been missing for over a month. Nobody had seen them, they hadn't even heard anything about them. They'd disappeared without a trace.

She wasn't handling it well. People had noticed it. Jack had noticed it...and he was worried.

"Maybe you should just...hold back on the drink"

Elizabeth looked towards Jack who was sat on the sofa next to her, his arm resting on the back of the sofa.

"I'm fine."

Jack shook his head

"You're drunk"

She'd been hitting the bottle a lot. Not a day went by when he didn't catch her drinking.

Elizabeth shook her head and sighed

"I am not drunk. I am...happy"

Jack sighed and closed his eyes

"'Lizabeth..." Jack stopped, he wasn't sure what to say, he didn't know what he could say. A month was a long time, escpecially after all she'd been through. She was thinking about the worst. Jack didn't know how he could help her. He wanted to help her.

Slowly he slid his hand down from the back of the sofa and gently rubbed her cheek.

"...He'll be okay"

A few tears fell from Elizabeth eyes. Jack's hand slid across and wiped the tears from her face.

"Something really bad as happened to them. I can feel it. I can feel it Jack. I just...I just wish that..."

She closed her eyes and more tears fell out. Her silent tears becoming violent sobs.

"Aiden...Steven...Carson... and now John, Rodney and Teyla."

Her voice was quiet but Jack could hear her. He moved closer to her and wrapped her in his arms, her head resting on his shoulder

"Shhh, They are coming home."

Elizabeth fell limp against Jack as her tears continued to fall. She seemed completely unaware of anything that was happening to her and gave no protest when Jack picked her up and carried her up the stairs to her bedroom.

Gently he placed her on the bed, kissing her forehead.

He turned to leave but felt himself being pulled back.

"Please...don't leave me"

Jack tensed and let out a breath. She needed him to be here with her. Hesitantly he walked back to the bed and slid down next to Elizabeth. He placed his arm across her waist and drew her slowly into him.

She buried her head in his chest, her tears still soaking through his shirt.

"Thank you Jack"

TBC...


End file.
